Saturday, April 30, 2011

What, you may be asking, is a 'geoid'? A geoid is the shape a totally flooded planet would take if it were solely influenced by gravity, and not by tides or currents or other factors. In other words, it's the 'sea level' of the entire planet.

Thanks to the work of European Space Agency (ESA) and their Gravity field and steady-state Ocean Circulation Explorer (GOCE), we have a pretty good map of Earth's geoid, shown below. Regions of highest gravity are raised yellow lumps (more water piles up in those areas) and regions of lowest gravity are seen as dark blue depressions.

Friday, April 29, 2011

Many comets originate in the Kuiper belt, a vast expanse of space extending beyond Neptune’s orbit.There, icy remnants from the formation of the solar system coalesce into comets, which are sometimes referred to as ‘dirty snowballs’.It has been presumed that comets never get warm enough to contain liquid water in their interiors.Data from NASA’s Stardust mission implies that that assumption may be wrong.

In 2004, the Stardust spacecraft approached the comet Wild-2, grabbed some molecules from its surface, and sent those particles down to Earth for analysis.The capsule containing those particles landed in 2006.Upon examination, researchers led by Eve Berger and Dante Lauretta of the University of Arizona found traces of minerals that form in the presence of liquid water.

In addition, the scientists found a rare mineral called cubanite in a variety that only exists below the boiling point of water. This set an upper limit to the temperatures that Wild-2 could have experienced.Knowing that the comet has stayed within the temperature range of liquid water has implications for the way comets form.

Thursday, April 28, 2011

Multicellular animals such as ourselves have a body plan consisting of distinct layers of cells. These germ cell layers are maintained as separate regions very early in embryonic development. New research by scientists from McGill University and from the University of Toronto has shed light on the process of differentiation and separation.

Our bodies are made up of three types of cells: ectoderm, mesoderm and endoderm. Broadly, ectoderm cells eventually make up the nervous system and skin; mesoderm cells become bone, muscle, and the blood system; and the endoderm develops into the gastrointestinal and respiratory tracts. Once the distinct layers are formed (at a time when the developing embryo is no more than a ball of cells), they remain separate for rest of the individual’s life.

Traditionally, it was thought that the three layers of cells remained separate due to differential attraction. It was proposed that endoderm cells, for example, had a higher affinity for other endoderm cells than for mesoderm or ectoderm cells. Thus, each type of cell would stick to its own kind in preference to other cell types. In this study, François Fagotto of McGill and Rudi Winklbauer of the University of Toronto took a closer look at developing frog embryos. They found that rather than simply adhering to their own types of cells, mesoderm and ectoderm cells were actively repelling each other.

Caption: These are frames from a high- resolution movie of live fluorescence confocal microscopy. The membranes (outlines) of ectoderm and mesoderm cells are labeled in green and orange, respectively. In the first frame, the two types of cells are in tight contact, and their membranes appear merged (green + orange = yellow). In frames 2 and 3, a repulsive reaction is triggered. While cells are being pulled away (arrows), adhesive contacts are ripped apart, leaving behind threads of membranes (arrowhead), just like when one tries to detach two objects that are glued together.

Credit: François Fagotto

Now it appears that both attraction and repulsion are important factors in embryo development.

Wednesday, April 27, 2011

This is actually a very difficult question.Besides being able to last for years without deteriorating or rotting, the food must be available in sufficient quantity to sustain the crew for that duration, and be palatable enough for the astronauts to choke down when they’re hungry.

Michele Perchonok from NASA Johnson Space Center and her colleagues have written a report detailing what kinds of foods a mission to Mars might take.Currently, each astronaut is provided with 3000 calories weighing 1.8 kg (food plus packaging) per day. That food is mostly ‘thermostabilized’ (heated to kill germs before packaging) or freeze-dried.Food scientists are continually fiddling with fat content and moisture levels in foods order to lower the weight of those items while preserving the number of calories.After all, any decrease in cargo weight also affects the weight of the fuel needed to lift that payload and lowers the cost of the whole mission.

Shelf life is another issue.Most foods that you see on supermarket shelves are not expected to last longer than two years (though some do).For a deep space mission, food might need to remain edible for at least five years without refrigeration.Therefore, NASA has been conducting shelf-life studies on a variety of foods.Of the 13 thermostabilized products they left out to rot, meat products fared the best and eggs the worst. They are also looking into the possibility of storing food outside the space craft, and using the cold vacuum of space to preserve the food.

Finally, the foods must be of sufficient variety and provide necessary nutrition for long missions, neither of which is easily accomplished.

I recently read Mary Roach’s book Packing for Mars: The Curious Science of Life in the Void, and it contains what is almost certainly more than you’d want to know about life in space.One of the sections deals with exactly this topic, how to stock a spacecraft’s pantry.One tip: use bite sized morsels. Any crumbs you create during your meal will float around you for the duration of your trip.

Tuesday, April 26, 2011

Bed bug infestations are on the rise in many regions of the world.Not only are they becoming more and more prevalent but they are also increasingly resistant to common pesticides.Luckily, help may be on the way in form of a natural pheromone.

Pheromones are chemical signals that are passed through the air like smells.Bed bugs rely on these signals to communicate with one another about reproductive readiness and other social cues.Researchers from Lund University and from the Engineering and Mathematics Mid Sweden University have discovered that among the pheromones produced by bed bugs is an alarm signal that causes other bed bugs to flee the area.Even better, the signal appears to work well on both the common bed bug Cimex lectularius and on the more recently introduced tropical bed bug Cimex hemipterus.

Getting bed bugs to evacuate your bed is certainly desirable, but if you can’t get your hands on any 4-oxo-(E)-2-hexenal or 4-oxo-(E)-2-octenal (the nymph alarm pheromones) you may prefer the following tips to avoid bringing home an infestation in the first place, especially if you frequent hotel rooms.

In the hotel room, check for signs of bed bug infestation—exoskeletons or small blood stains.Not an easy task since bed bugs are no more than half a centimeter long.You’ll need to pull back the sheets and look along the seam lines of the mattress and box springs.You should also check around the headboard, particularly in screw holes or carved recesses.

Keep your suitcases off the carpet (some sites suggest keeping your luggage in the bathtub), and check them for infestation before returning home.

In order to specifically identify the gene changes that were unique to the cancers, the scientists compared the DNA in the tumors to the DNA of the same patients’ healthy cells. That way, exact genetic comparisons could be made between healthy tissue and cancerous tissue within each person. Considering that each genome was sequenced 30 times to ensure accuracy, the entire project required the sequencing of over 10 trillion base pairs.

In all there were over 1700 mutations in the tumor genomes, though many may not have been specifically related to the cancer. Only five mutations were each found in over 10% of the tumors, and one of them was present in 40% of the tumors (some tumors had more than one of these common mutations). Of course, a gene disruption that is only found in one woman out of 50 may still be responsible for thousands of cases of breast cancer in the general public, or may be more common in other types of cancer.

Only women with estrogen-receptor-positive breast cancer were recruited for this study. Although all were given estrogen-lowering drugs in an attempt to slow their tumor growth, only about half the women responded to this treatment. The scientists are hopeful that among other things, this study will help doctors figure out when to offer specific treatment regiments like estrogen suppression.

Caption: The above Circos plot is a visual representation of the genomic disruptions in one of the breast cancers studied.

Sunday, April 24, 2011

Up to 10% of the population is allergic to cats. Mark Larché, the Canada Research Chair in Allergy & Immune Tolerance, and his colleagues have been working to help those people.In doing so, they not only created a cat allergy vaccine, but they are pioneering work on vaccines against other common allergens.

Allergic reactions result when patients’ immune systems attack innocuous substances, such as pollen or animal dander.Instead of ignoring such substances, the body produces a particular type of antibody called immunoglobulin E (IgE), which in turn leads to the release of the histamines and other chemicals that cause allergic symptoms.

Traditionally, there are two ways to treat cat allergies:avoiding cats, and getting allergen specific immunotherapy, a.k.a. allergy shots. Although the exact mechanism of how allergy shots work is not completely understood, it appears that repeated exposure to the allergens both desensitizes the immune system and increases the amount of a different type of antibody (IgG) which can outcompete IgE.Allergy shots can be highly effective, but they are also time consuming, expensive and uncomfortable.Most people must get shots as often as twice a week at first, and continue to get shots for several years.

Larché and his team chose a different approach.Rather than injecting patients with increasing doses of whole allergen, the researchers injected volunteers with synthetic peptides created from a cat protein that is known to be responsible for the majority of allergic symptoms.The peptide vaccine activated T-cells, and unlike allergen immunotherapy, did not stimulate the release of histamines.Nonetheless, the treatment resulted in insensitivity to cat allergen skin tests.

The required dosage to achieve effectiveness has yet to be worked out.Allergy sufferers will probably need multiple doses of the peptide vaccine to be symptom-free and it’s not clear how long the treatment will continue to work.On the plus side, peptide immunotherapy does not appear to cause the side affects associated with traditional immunotherapy (soreness and swelling at the injection site, or systemic reactions in severe cases).Whether the technique is also time and/or cost effective is yet to be determined.

Saturday, April 23, 2011

Think humans have good memories? Watch Ayumu, a young male chimpanzee perform a seemingly impossible memory task. He has to touch the squares on the screen in the correct numerical order after having seen the numbers for only 210 milliseconds.

To be fair, other researchers have criticized this test, claiming that Ayumu had required extensive practice to achieve this result, and that human test subjects did as well or better with the same amount of practice.

Friday, April 22, 2011

Johns Hopkins researchers led by Emily Sydnor took a closer look at the hands-free faucets in hospitals and didn’t like what they found.The automatic faucets were up to three times as likely to be contaminated with Legionella bacteria as manual faucets.

This is counterintuitive to say the least.After all, the whole point of the hands-free faucets was to prevent contamination.The researchers themselves are puzzled as to why the electronic-eye fixtures, which have been in hospitals for over a decade, are so problematic.One possible reason may be that the hands-free faucets have more complicated valve and electronic components that cannot be effectively disinfected.Many hospitals treat their water supply specifically to reduce the levels of Legionella and other harmful pathogens.Those methods don’t appear to work on the electronic faucets, which can apparently harbor harmful levels of bacteria.

The researchers have contacted the faucet manufacturers to see if modifications can be made to allow the hands-free devices to be more thoroughly sterilized.In the meantime, Johns Hopkins Hospital is replacing its automatic faucets with manual ones.Unfortunately, this means the hospital will have to go back to using four times as much water for hand washing.

By the way, Sydnor does not think the general public has anything to fear from non-touch faucets in public venues:

The levels of bacterial growth in the electronic faucets, particularly the Legionella spp., were of concern because they were beyond the tolerable thresholds determined by the hospital. Exposure to Legionella spp. is dangerous for chronically ill or immune compromised patients because it may cause pneumonia in these vulnerable patients. The levels we found of Legionella spp. were still within the level that is well tolerated by healthy individuals.

Perhaps because AIDS is a largely manageable disease today and no longer the death sentence it once was, hundreds of HIV-positive patients now languish on organ donor lists, sometimes for years. The very medications that are prolonging their lives can sometimes cause severe enough damage to their livers and/or kidneys to require organ replacement. In general, those lucky enough to receive new organs have had good outcomes. The hard part is to survive long enough to be matched with a donor.

In the meantime, an equivalent number of HIV infected people with transplantable organs die each year. If those organs were given to the HIV infected patients on the donor list, not only would there be enough to go around, but it would free up the non-HIV infected organs for HIV-negative recipients.

There are a few major problems to be overcome before this practice can be sanctioned. First, precautions must be in place to ensure that no HIV organs get accidentally transplanted into HIV-negative patients. Second, doctors must take care not to introduce more aggressive strains of HIV into their patients.

Sergev and his team are confident that these safeguards can be met. They draw on lessons learned from transplanting hepatitis C infected organs only into hepatitis C infected recipients, a practice that has been highly successful. A change in HIV donation policy would require an act of Congress, who might take some convincing.

Wednesday, April 20, 2011

Most people do not care for bitter foods.About a quarter of people are ‘supertasters’ who are particularly sensitive to bitter tastes.Unfortunately, those people may find many nutritious foods such as leafy greens or tea unpalatable.Enter GIV3616, a bitter blocker or compound that blocks bitter taste receptors, presented by Ioana Ungureanu from the Givaudan Flavors Corporation at the 2011 National Meeting & Exposition of the American Chemical Society (ACS).

There are actually some 27 different varieties of bitter taste receptor.Ungureanu was previously responsible for the compound GIV3727 that specifically inhibited the taste receptors responsible for the bitter aftertaste of saccharin.GIV3616 is less specific and more powerful.It can also be readily dissolved into foods and beverages.

According to Ungureanu:

It works at levels on the order of parts per million and blocks flavors using 10 times less material than what was needed previously.

Apart from making vegetables more agreeable, bitter blockers like GIV3616 might help people swallow needed medication or help those with poor appetites improve their diets.

Apparently, inducing abortion was not the first choice of most mares.If possible, returning pregnant mares did their best to mate with the local males, especially the most dominant ones.Those that were able to mate with local males did not abort their fetuses, whereas mares that were prevented from mating with males aborted in great numbers.

The authors speculate that the females are using this strategy to avoid wasting their time and energy on an infant that is likely to be killed by the dominant male in the group.In many types of animals, males will routinely kill the offspring of other males.For example, when a new male lion takes over a pride, he will immediately kill all the cubs that had been the progeny of the previous pride master.This brings the females into estrus much more quickly so that they can get to work producing the new lion’s offspring.

The domestic mares returning from a foreign assignation may be mating with the local dominant males in an attempt to confuse paternity.Barring that, they may abort the fetus.This suggests that breeders should encourage returning pregnant mares to mate with the local males.It’s really a win-win for everybody.

Monday, April 18, 2011

Daniel Nocera and his colleagues from MIT debuted the first practical artificial leaf at the 2011 National Meeting of the American Chemical Society. Their version is cheap, effective and stable, overcoming in one swoop the three major problems of previous attempts to make artificial leaves.

The point of making artificial leaves (a.k.a. solar cells) is to generate cheap, clean energy. Nocera’s device does just that with a minimum of components: a thin wafer of silicon containing catalysts made of nickel and cobalt, a gallon of water, and sunlight. When those three components are combined, the catalysts in the wafer split the water into hydrogen and oxygen gases, which are then stored in fuel cells and ultimately used to generate electricity.

Compared to earlier incarnations of artificial leaves, beginning with the model John Turner (U.S. National Renewable Energy Laboratory) designed a decade ago, Nocera’s prototype shows real promise for widespread functionality. It is already ten times more efficient that natural leaves, a benchmark Nocera expects to be able to raise in the future. In addition, each slip of silicon can function continuously for over 45 hours. I assume they tested this feature with artificial light, rather than moving their sample around the Earth for two days.

The two types of illusions they used are known as the Ponzo illusion (pictured left) and the Ebbinghaus illusion (pictured right).In the former illusion, objects that seem to be more distant appear larger than identically sized objects that seem to be closer, and in the latter illusion, identically sized central objects appear to be of different sizes depending on the size of the surrounding objects.

The researchers devised the two illusions so that the identically sized test objects (central circles or horizontal bars) could be displayed to either one eye, or separately to two different eyes. Six volunteers were asked to look through the apparatuses and give information about the perceived size of the test object (circle or bar) as compared to the reference object.The Ponzo illusion (horizontal bars) was just as effective regardless of whether one or two eyes received the information, but the Ebbinghaus illusion (circle sizes) became much weaker when the circles were seen by different eyes.

The authors suggest that two different mechanisms are at work in interpreting the visual signals from the illusions.The Ponzo illusion relies on assumptions about depth and distance in three dimensions, whereas the Ebbinghaus illusion is based on a simple size comparison. For this reason, the two illusions may be dependent on different types of neurons, specifically binocular versus monocular neurons.

Friday, April 15, 2011

Jill Pecon-Slattery of the National Cancer Institute has led an international team of biologists in refining our family tree. The result, pictured below, is the most comprehensive genetic comparison to date. In case you’re having difficulty locating humans, we’re ‘Homo’, in the purple color group.

The molecular phylogeny of 61 Primate genera, two Dermoptera genera, and one Scandentia genus and rooted by Lagomorpha.

The authors sequenced 54 nuclear genes from 186 different primates to come up with their chart.The differences and similarities between species not only demonstrate current levels of relatedness, but also shed light on the evolutionary history of primates, a topic of great interest to us fellow primates.Perhaps more importantly, the information could yield insight into our susceptibility to certain pathogens or environmental hazards.

Thursday, April 14, 2011

Synesthesia is a cross-firing of the senses. For example, a person may perceive particular digits to have specific colors, sounds, shapes or even personalities.One of the more common forms of synesthesia is called grapheme, or color synesthesia, in which the synthesthete sees each letter or number as an exact shade that can be picked out of a color chart.However, people who have grapheme can also identify the physical color of the letter, that is, the color of the ink.How do synthesthetes see in two colors at once?Bruno Laeng , Kenneth Hugdahland Karsten Specht from the Universities of Oslo and Bergen found that synthesthetes use the same parts of the brain to process the two kinds of color.

The researchers put two such volunteers in an fMRI to see which parts of their brains were responsible for identifying the different colors.In some cases, they gave the subjects letters or numbers that were physically colored (via the wavelength of the ink) the same shade that that person perceived the letter or number to be.In other cases, the ink color was completely different from the perceived color.In all trials, the same part of the brain was activated, namely the color processing part of the brain.In other words, the information about the color produced by the ink’s wavelength and the ‘imagined’ synesthetic color were both processed by the brain in the same way.

This indicates that synthesthetes feel as if they are really seeing both colors equally; not something the rest of us can easily understand.

Wednesday, April 13, 2011

Contrary to conventional wisdom, the color of one’s phlegm is not a good indicator of whether one would benefit from taking antibiotics. So says a new study by a European consortium of scientists led by Chris Butler of Cardiff University.

Many patients and physicians believe that coughing up yellow or green sputum is indicative of a bacterial infection that can be successfully treated with antibiotics, whereas coughing up clear or no phlegm might be more diagnostic of an illness that cannot be treated with antibiotics. In this study, two sets of comparisons were made.

First, is colored phlegm associated with feeling ill and/or with antibiotic prescription? In other words, do patients presenting with green phlegm tend to feel worse than patients with clear phlegm? And how often do the two groups receive prescriptions for antibiotics? Not surprisingly, antibiotics were most often given to patients with colored phlegm. However, those patients did not report more severe symptoms than the patients with no sputum (who had not received prescriptions).

Second, the researchers asked whether the antibiotics actually did alleviate symptoms more often in patients with colored sputum (who were presumably suffering from bacterial infections) than in those with clear or no sputum. The answer was ‘no’. Neither the color of the sputum patients coughed up nor the magnitude of their symptoms was predictive of whether they had bacterial infections that could benefit from antibiotic treatment.

I love reading stories that show that I’ve been wrong about something. It highlights exactly why you can’t take things for granted, but must actually study them. And sorry, no pretty pictures with this post.

Salamander embryos grow inside egg capsules that are covered with and usually infiltrated by a type of green algae.

Credit: Courtesy of Roger Hangarter

Endosymbiosis, like other types of symbiosis, involves a close relationship between two different species. The twist here is that one of the organisms resides within the very cells of the other. Although this kind of relationship is not uncommon among simpler organisms, this is a first for vertebrates, whose immune systems usually fight off any such invasion.

The relationship between O. amblystomatis andspotted salamanders has been observed for more than a century. Each organism grows more slowly in the absence of the other. It wasn’t until the modern techniques of using gene specific probes and fluorescence microscopy became available that scientists could see that the algae were actually inside the cells of the salamander embryos.

The salamanders appear to lose their algae once they hatch from their egg capsules. Presumably, the benefit gained by maintaining the endosymbiants is diminished once the animals are able to gather their own food.

Caption: Spotted salamanders are the first known vertebrate to have an endosymbiont. The salamanders are found throughout eastern North America.

Credit: Courtesy of Roger Hangarter

Roger Hangarter of Indiana University makes this observation about the spotted salamander, which is a common backyard occupant in many parts of North America:

I think it is important for people to realize that you do not need to go to exotic locations to make interesting scientific discoveries.

Stochastic Scientist? What's up with that?

Why the Stochastic Scientist? As I'm sure you all know, 'stochastic' is another word for 'random', which is what I intend for the focus of this blog. Although my formal training is as a molecular biologist, there are many other fields of science that are also fascinating and beautiful. It's my intention to blog about which ever scientific discovery or invention catches my, and hopefully your, fancy.

I also hope to inspire people to learn more about science. By choosing among a huge variety of scientific endeavors, I'll undoubtably hit upon something that will pique my readers' interest.

I guess I could have called my blog 'The Joy of Science', but that wouldn't have been quite so random.